I have a site with about 30,000 posts and the custom taxonomy count was off. After running this plugin a few times the taxonomy count actually got worse. I had to run it a few times because it timed out.
Not worry, though. I used the following SQL to fix the problem and it ran very quickly.
9300 rows affected. (Query took 2.9573 seconds.)
UPDATE wp_term_taxonomy SET count = ( SELECT COUNT(*) FROM wp_term_relationships rel LEFT JOIN wp_posts po ON (po.ID = rel.object_id) WHERE rel.term_taxonomy_id = wp_term_taxonomy.term_taxonomy_id AND wp_term_taxonomy.taxonomy NOT IN ('link_category') AND po.post_status IN ('publish', 'future') )
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